RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11302
(764 letters)
>gnl|CDD|216920 pfam02182, YDG_SRA, YDG/SRA domain. The function of this domain is
unknown, it contains a conserved motif YDG after which
it has been named.
Length = 154
Score = 204 bits (521), Expect = 7e-62
Identities = 81/172 (47%), Positives = 100/172 (58%), Gaps = 25/172 (14%)
Query: 418 HFGPIPGIEVGQSYLYRFQASEAGVHRPHVSGIHGREDVG---AFSLVLSGGYEDDVDDG 474
G +PG+EVG + YR + G+HRPH +GI G + G A S+V SGGYEDD D+G
Sbjct: 2 RIGHVPGVEVGDIFFYRVELCVVGLHRPHQAGIDGMKSEGGTIATSIVSSGGYEDDEDNG 61
Query: 475 DSFLYTGSGGRDLSGNKRTSVQSFDQTLTRMNKALARNCNAPIDDKRGNEAVDWKKGKPV 534
D +YTG GG DLSGNK QS DQ L R N ALA +C +KG PV
Sbjct: 62 DVLVYTGQGGNDLSGNK----QSEDQKLERGNLALANSC---------------RKGNPV 102
Query: 535 RVMRNFHGAKHSKYAPKEG-NRYDGIYKVVKYYPVKGSSDFIVWRFHLQRDD 585
RV+R G S +APK G RYDG+Y+V KY+ KG S F V++F L R
Sbjct: 103 RVIRGEKG--PSSHAPKGGIYRYDGLYRVEKYWREKGKSGFKVFKFKLVRIP 152
>gnl|CDD|197742 smart00466, SRA, SET and RING finger associated domain. Domain of
unknown function in SET domain containing proteins and
in Deinococcus radiodurans DRA1533.
Length = 155
Score = 186 bits (475), Expect = 2e-55
Identities = 77/172 (44%), Positives = 96/172 (55%), Gaps = 26/172 (15%)
Query: 418 HFGPIPGIEVGQSYLYRFQASEAGVHRPHVSGIHGREDV----GAFSLVLSGGYEDDVDD 473
FGP+PG+EVG + YR + G+HRP +GI G E GA S+V SGGYEDD DD
Sbjct: 4 IFGPVPGVEVGDIFFYRVELCLVGLHRPTQAGIDGLESDEGEPGATSVVSSGGYEDDTDD 63
Query: 474 GDSFLYTGSGGRDLSGNKRTSVQSFDQTLTRMNKALARNCNAPIDDKRGNEAVDWKKGKP 533
GD +YTG GGRD T Q DQ L R N AL +C KG P
Sbjct: 64 GDVLIYTGQGGRD-----MTHGQPEDQKLERGNLALEASCR---------------KGIP 103
Query: 534 VRVMRNFHGAKHSKYAPKEGNRYDGIYKVVKYYPVKGSSDFIVWRFHLQRDD 585
VRV+R G +SKYAP +G YDG+Y++V Y+ G S F+V++F L R
Sbjct: 104 VRVVRGMKG--YSKYAPGKGYIYDGLYRIVDYWREVGKSGFLVFKFKLVRIP 153
>gnl|CDD|176392 cd01797, NIRF_N, amino-terminal ubiquitin-like domain of Np95
and NIRF. NIRF_N This CD represents the
amino-terminal ubiquitin-like domain of a family of
nuclear proteins that includes Np95 and NIRF
(Np95/ICBP90-like RING finger) protein. Both Np95 and
NIRF have a domain architecture consisting of a
ubiquitin-like domain, a PHD finger, a YDG/SRA domain,
Rb-binding motifs and a RING finger domain. Both Np95
and NIRF are ubiquitin ligases that ubiquitinate PCNP
(PEST-containing nuclear proteins). While Np95 is
capable of binding histones, NIRF is involved in cell
cycle regulation.
Length = 78
Score = 89.1 bits (221), Expect = 1e-21
Identities = 34/78 (43%), Positives = 57/78 (73%), Gaps = 1/78 (1%)
Query: 1 MYVKIRSLDGSKNC-VLVLSKRTLISDMKTQIENTLDVPVDKQRLFYKGKQLEDEYMLFD 59
M++++R++DG + V LS+ T + +++ +I+ +V + QRLFY+GKQ+ED + LFD
Sbjct: 1 MWIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYRGKQMEDGHTLFD 60
Query: 60 YNVNLNDVIQLMIKADID 77
YNV LND+IQL+++ D D
Sbjct: 61 YNVGLNDIIQLLVRQDPD 78
>gnl|CDD|152583 pfam12148, DUF3590, Protein of unknown function (DUF3590). This
domain is found in eukaryotes, and is typically between
83 and 97 amino acids in length. It is found in
association with pfam00097, pfam02182, pfam00628,
pfam00240. There are two conserved sequence motifs: RAR
and NYN. The domain is part of the protein NIRF which
has zinc finger and ubiquitinating domains. The function
of this domain is likely to be mainly structural,
however this has not been confirmed.
Length = 85
Score = 69.0 bits (169), Expect = 2e-14
Identities = 33/90 (36%), Positives = 54/90 (60%), Gaps = 5/90 (5%)
Query: 135 YVDAILETEGAWFESQITHILVDINKEKPYDEDDLIFKVVHLKYKDDGSSTMKFDDIRPL 194
+DA GAWFE+Q+ V + K+ +++D+I+ V + Y ++G M D+RP
Sbjct: 1 LIDARDNNMGAWFEAQV----VTVTKKALAEDEDVIYHVKYDDYPENGVVQMTGKDVRPR 56
Query: 195 PKHLITEFNENLIGVRVMGNYNAEEPRERG 224
+ L+ ++NE +G VM NYN +EP+ERG
Sbjct: 57 ARTLL-KWNELEVGQVVMVNYNPDEPKERG 85
>gnl|CDD|214563 smart00213, UBQ, Ubiquitin homologues. Ubiquitin-mediated
proteolysis is involved in the regulated turnover of
proteins required for controlling cell cycle
progression.
Length = 72
Score = 60.0 bits (146), Expect = 2e-11
Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 1 MYVKIRSLDGSKNCVLVLSKRTLISDMKTQIENTLDVPVDKQRLFYKGKQLEDEYMLFDY 60
+ + +++LDG K L + +S++K +I +P ++QRL YKGK LED+ L DY
Sbjct: 1 IELTVKTLDG-KTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADY 59
Query: 61 NVNLNDVIQLMIK 73
+ I L+++
Sbjct: 60 GIQDGSTIHLVLR 72
>gnl|CDD|214584 smart00249, PHD, PHD zinc finger. The plant homeodomain (PHD)
finger is a C4HC3 zinc-finger-like motif found in
nuclear proteins thought to be involved in epigenetics
and chromatin-mediated transcriptional regulation. The
PHD finger binds two zinc ions using the so-called
'cross-brace' motif and is thus structurally related to
the RING finger and the FYVE finger. It is not yet known
if PHD fingers have a common molecular function. Several
reports suggest that it can function as a
protein-protein interacton domain and it was recently
demonstrated that the PHD finger of p300 can cooperate
with the adjacent BROMO domain in nucleosome binding in
vitro. Other reports suggesting that the PHD finger is a
ubiquitin ligase have been refuted as these domains were
RING fingers misidentified as PHD fingers.
Length = 47
Score = 59.1 bits (143), Expect = 2e-11
Identities = 18/46 (39%), Positives = 25/46 (54%)
Query: 319 CSICAGKTSPDKLIVCEECQHYYHIWCLKPPLESVPEDDEWFCPSC 364
CS+C +L+ C+ C +YH CL PPL D +W+CP C
Sbjct: 2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
>gnl|CDD|176364 cd01769, UBL, Ubiquitin-like domain of UBL. UBLs function by
remodeling the surface of their target proteins,
changing their target's half-life, enzymatic activity,
protein-protein interactions, subcellular localization
or other properties. At least 10 different
ubiquitin-like modifications exist in mammals, and
attachment of different ubls to a target leads to
different biological consequences. Ubl-conjugation
cascades are initiated by activating enzymes, which
also coordinate the ubls with their downstream
pathways.
Length = 69
Score = 57.3 bits (139), Expect = 1e-10
Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 4 KIRSLDGSKNCVLVLSKRTLISDMKTQIENTLDVPVDKQRLFYKGKQLEDEYMLFDYNVN 63
+++L G + V T ++++K +I VP ++QRL Y GK L+D+ L DY +
Sbjct: 1 TVKTLTGKTFELEVSPDDT-VAELKAKIAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQ 59
Query: 64 LNDVIQLMIK 73
+ L+++
Sbjct: 60 DGSTLHLVLR 69
>gnl|CDD|215813 pfam00240, ubiquitin, Ubiquitin family. This family contains a
number of ubiquitin-like proteins: SUMO (smt3
homologue), Nedd8, Elongin B, Rub1, and Parkin. A
number of them are thought to carry a distinctive
five-residue motif termed the proteasome-interacting
motif (PIM), which may have a biologically significant
role in protein delivery to proteasomes and recruitment
of proteasomes to transcription sites.
Length = 69
Score = 57.2 bits (139), Expect = 2e-10
Identities = 23/68 (33%), Positives = 41/68 (60%), Gaps = 1/68 (1%)
Query: 6 RSLDGSKNCVLVLSKRTLISDMKTQIENTLDVPVDKQRLFYKGKQLEDEYMLFDYNVNLN 65
++LDG + V T +S++K +IE+ +PVD+QRL + GK LED+ L +Y +
Sbjct: 1 KTLDGKTITLEVDPSDT-VSELKEKIEDKEGIPVDQQRLIFSGKVLEDDTTLSEYGIQDG 59
Query: 66 DVIQLMIK 73
+ L+++
Sbjct: 60 STLHLVLR 67
>gnl|CDD|201356 pfam00628, PHD, PHD-finger. PHD folds into an interleaved type of
Zn-finger chelating 2 Zn ions in a similar manner to
that of the RING and FYVE domains. Several PHD fingers
have been identified as binding modules of methylated
histone H3.
Length = 51
Score = 56.7 bits (137), Expect = 2e-10
Identities = 18/50 (36%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 319 CSICAGKTSPDKLIVCEECQHYYHIWCLKPPLESVPE-DDEWFCPSCKRD 367
C++C +L++C+ C ++H+ CL PPLE + EW+CP CK
Sbjct: 2 CAVCGKVDDDGELLLCDGCDRWFHLACLGPPLEPEEIPEGEWYCPECKPK 51
>gnl|CDD|176402 cd01807, GDX_N, ubiquitin-like domain of GDX. GDX contains an
N-terminal ubiquitin-like domain as well as an
uncharacterized c-terminal domain. The function of GDX
is unknown.
Length = 74
Score = 53.0 bits (127), Expect = 6e-09
Identities = 24/73 (32%), Positives = 46/73 (63%), Gaps = 1/73 (1%)
Query: 1 MYVKIRSLDGSKNCVLVLSKRTLISDMKTQIENTLDVPVDKQRLFYKGKQLEDEYMLFDY 60
M++ ++ L G + C L +S++ +S +K + L+VP ++QRL +KGK L D+ L DY
Sbjct: 1 MFLTVKLLQG-RECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADDKRLSDY 59
Query: 61 NVNLNDVIQLMIK 73
++ N + L+++
Sbjct: 60 SIGPNAKLNLVVR 72
>gnl|CDD|176404 cd01809, Scythe_N, Ubiquitin-like domain of Scythe protein.
Scythe protein (also known as Bat3) is an apoptotic
regulator that is highly conserved in eukaryotes and
contains a ubiquitin-like domain near its N-terminus.
Scythe binds reaper, a potent apoptotic inducer, and
Scythe/Reaper are thought to signal apoptosis, in part
through regulating the folding and activity of
apoptotic signaling molecules.
Length = 72
Score = 49.9 bits (120), Expect = 5e-08
Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 1/68 (1%)
Query: 3 VKIRSLDGSKNCVLVLSKRTLISDMKTQIENTLDVPVDKQRLFYKGKQLEDEYMLFDYNV 62
+K+++LD S+ + + + D+K +I + +PV++QRL Y G+ L+D+ L +Y V
Sbjct: 3 IKVKTLD-SQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDDETLSEYKV 61
Query: 63 NLNDVIQL 70
I L
Sbjct: 62 EDGHTIHL 69
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 48.2 bits (115), Expect = 1e-07
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 7/48 (14%)
Query: 691 CIICQELVY---KPITLDCVHTFCHDCLKRAFKIESDACNSCPYCRKE 735
C IC + + + L C H F +CL + + N+CP CR
Sbjct: 3 CPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRS----SNTCPLCRAP 46
Score = 35.8 bits (83), Expect = 0.003
Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 5/49 (10%)
Query: 319 CSICAGKTSPDKLIVCEECQHYYHIWCLKPPLESVPEDDEWFCPSCKRD 367
C IC + P + +V C H +H CL L S CP C+
Sbjct: 3 CPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNT-----CPLCRAP 46
>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin. Ubiquitin (includes Ubq/RPL40e
and Ubq/RPS27a fusions as well as homopolymeric
multiubiquitin protein chains).
Length = 76
Score = 47.9 bits (114), Expect = 4e-07
Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 1 MYVKIRSLDGSKNCVLVLSKRTLISDMKTQIENTLDVPVDKQRLFYKGKQLEDEYMLFDY 60
M + +++L G K L + I ++K +I++ +P D+QRL + GKQLED L DY
Sbjct: 1 MQIFVKTLTG-KTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY 59
Query: 61 NVNLNDVIQLMIK 73
N+ + L+++
Sbjct: 60 NIQKESTLHLVLR 72
>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain, a
specialized type of Zn-finger of 40 to 60 residues that
binds two atoms of zinc; defined by the 'cross-brace'
motif C-X2-C-X(9-39)-C-X(1-3)-
H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved
in mediating protein-protein interactions; identified in
a proteins with a wide range of functions such as viral
replication, signal transduction, and development; has
two variants, the C3HC4-type and a C3H2C3-type (RING-H2
finger), which have different cysteine/histidine
pattern; a subset of RINGs are associated with B-Boxes
(C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
Length = 45
Score = 46.7 bits (111), Expect = 4e-07
Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 691 CIICQELVYKPITLD-CVHTFCHDCLKRAFKIESDACNSCPYCRKE 735
C IC E +P+ L C H FC C+ + K N+CP CR
Sbjct: 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGK---NTCPLCRTP 44
Score = 35.1 bits (81), Expect = 0.005
Identities = 12/50 (24%), Positives = 18/50 (36%), Gaps = 6/50 (12%)
Query: 319 CSICAGKTSPDKLIVCEECQHYYHIWCLKPPLESVPEDDEWFCPSCKRDT 368
C IC + +V C H + C+ L+S CP C+
Sbjct: 2 CPIC--LEEFREPVVLLPCGHVFCRSCIDKWLKSGK----NTCPLCRTPI 45
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 46.7 bits (111), Expect = 4e-07
Identities = 19/49 (38%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 687 EKFLCIICQELVYKPITL-DCVHTFCHDCLKRAFKIESDACNSCPYCRK 734
E+ C IC +L+ P+ L C H FC +C+ R K +S CP CR
Sbjct: 1 EELECPICLDLLRDPVVLTPCGHVFCRECILRYLKKKS----KCPICRT 45
Score = 29.0 bits (65), Expect = 0.95
Identities = 11/48 (22%), Positives = 17/48 (35%), Gaps = 7/48 (14%)
Query: 319 CSICAGKTSPDKLIVCEECQHYYHIWCLKPPLESVPEDDEWFCPSCKR 366
C IC +V C H + C+ L+ + CP C+
Sbjct: 5 CPIC--LDLLRDPVVLTPCGHVFCRECILRYLKKKSK-----CPICRT 45
>gnl|CDD|176352 cd00196, UBQ, Ubiquitin-like proteins. Ubiquitin homologs;
Includes ubiquitin and ubiquitin-like proteins.
Ubiquitin-mediated proteolysis is part of the regulated
turnover of proteins required for controlling cell
cycle progression. Other family members are protein
modifiers that perform a wide range of functions.
Ubiquitination usually results in a covalent bond
between the C-terminus of ubiquitin and the
epsilon-amino group of a substrate lysine. The
three-step mechanism requires an activating enzyme (E1)
that forms a thiol ester with the C-terminal carboxy
group, a conjugating enzyme (E2) that transiently
carries the activated ubiquitin molecule as a thiol
ester, and a ligase (E3) that transfers the activated
ubiquitin from the E2 to the substrate lysine residue.
In poly-ubiquitination, ubiquitin itself is the
substrate.
Length = 69
Score = 44.8 bits (106), Expect = 4e-06
Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 4 KIRSLDGSKNCVLVLSKRTLISDMKTQIENTLDVPVDKQRLFYKGKQLEDEYMLFDYNVN 63
K++ DG +LV S T ++D+K ++ L +P ++QRL GK L D L DY +
Sbjct: 1 KVKLNDGKTVELLVPSGTT-VADLKEKLAKKLGLPPEQQRLLVNGKILPDSLTLEDYGLQ 59
Query: 64 LNDVIQLMIK 73
D + L+ +
Sbjct: 60 DGDELVLVPR 69
>gnl|CDD|214546 smart00184, RING, Ring finger. E3 ubiquitin-protein ligase
activity is intrinsic to the RING domain of c-Cbl and is
likely to be a general function of this domain; Various
RING fingers exhibit binding activity towards E2
ubiquitin-conjugating enzymes (Ubc' s).
Length = 40
Score = 42.1 bits (99), Expect = 1e-05
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 4/43 (9%)
Query: 691 CIICQELVYK-PITLDCVHTFCHDCLKRAFKIESDACNSCPYC 732
C IC E K P+ L C HTFC C+++ + + N+CP C
Sbjct: 1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLESGN---NTCPIC 40
Score = 32.5 bits (74), Expect = 0.036
Identities = 14/46 (30%), Positives = 17/46 (36%), Gaps = 6/46 (13%)
Query: 319 CSICAGKTSPDKLIVCEECQHYYHIWCLKPPLESVPEDDEWFCPSC 364
C IC K V C H + C++ LES CP C
Sbjct: 1 CPIC--LEEYLKDPVILPCGHTFCRSCIRKWLES----GNNTCPIC 40
>gnl|CDD|176400 cd01805, RAD23_N, Ubiquitin-like domain of RAD23. RAD23 belongs
to a family of adaptor molecules having affinity for
both the proteasome and ubiquitinylated proteins and
thought to shuttle these ubiquitinylated proteins to
the proteasome for destruction. RAD23 interacts with
ubiquitin through its C-terminal ubiquitin-associated
domains (UBA) and with the proteasome through its
N-terminal ubiquitin-like domain (UBL).
Length = 77
Score = 43.1 bits (102), Expect = 2e-05
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 1 MYVKIRSLDGSKNCVLVLSKRTLISDMKTQIENT--LDVPVDKQRLFYKGKQLEDEYMLF 58
M + ++L + V T ++++K +IE D P ++Q+L Y GK L+D+ L
Sbjct: 1 MKITFKTLKQQTFPIEVDPDDT-VAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLE 59
Query: 59 DYNVNLNDVIQLMIK 73
+Y ++ D + +M+
Sbjct: 60 EYKIDEKDFVVVMVS 74
>gnl|CDD|240069 cd04718, BAH_plant_2, BAH, or Bromo Adjacent Homology domain,
plant-specific sub-family with unknown function. BAH
domains are found in a variety of proteins playing roles
in transcriptional silencing and the remodeling of
chromatin. It is assumed that in most or all of these
instances the BAH domain mediates protein-protein
interactions.
Length = 148
Score = 43.3 bits (102), Expect = 8e-05
Identities = 18/44 (40%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 341 YHIWCLKPPLESVPEDDEWFCPSCKRDTSEVIAPGQKLKDSKKK 384
+H+ CL+PPL+ VPE D W CP C+ + S A Q S+
Sbjct: 2 FHLCCLRPPLKEVPEGD-WICPFCEVEKSGQSAMPQLPPTSRSA 44
>gnl|CDD|176401 cd01806, Nedd8, Nebb8-like ubiquitin protein. Nedd8 (also known
as Rub1) has a single conserved ubiquitin-like domain
that is part of a protein modification pathway similar
to that of ubiquitin. Nedd8 modifies a family of
molecular scaffold proteins called cullins that are
responsible for assembling the ROC1/Rbx1 RING-based E3
ubiquitin ligases, of which several play a direct role
in tumorigenesis.
Length = 76
Score = 40.9 bits (96), Expect = 9e-05
Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 1 MYVKIRSLDGSKNCVLVLSKRTLISDMKTQIENTLDVPVDKQRLFYKGKQLEDEYMLFDY 60
M +K+++L G K + + + +K ++E +P +QRL Y GKQ+ D+ DY
Sbjct: 1 MLIKVKTLTG-KEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDDKTAADY 59
Query: 61 NVNLNDVIQLMI 72
+ V+ L++
Sbjct: 60 KLEGGSVLHLVL 71
>gnl|CDD|176395 cd01800, SF3a120_C, Ubiquitin-like domain of Mammalian splicing
factor SF3a_120. SF3a120_C Mammalian splicing factor
SF3a consists of three subunits of 60, 66, and 120 kDa
and functions early during pre-mRNA splicing by
converting the U2 snRNP to its active form. The 120kDa
subunit (SF3a120) has a carboxy-terminal ubiquitin-like
domain and two SWAP (suppressor-of-white-apricot)
domains, referred to collectively as the SURP module,
at its amino-terminus.
Length = 76
Score = 40.5 bits (95), Expect = 2e-04
Identities = 16/50 (32%), Positives = 27/50 (54%)
Query: 24 ISDMKTQIENTLDVPVDKQRLFYKGKQLEDEYMLFDYNVNLNDVIQLMIK 73
+S +K +I +P KQ+L Y+G ++D L YN+ +I L +K
Sbjct: 20 VSVLKVKIHEETGMPAGKQKLQYEGIFIKDSNSLAYYNLANGTIIHLQLK 69
>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18. All proteins in this
family for which functions are known are involved in
nucleotide excision repair.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 397
Score = 44.2 bits (104), Expect = 2e-04
Identities = 23/83 (27%), Positives = 35/83 (42%), Gaps = 10/83 (12%)
Query: 682 LEHIQEKFLCIICQELVYKPITLDCVHTFCHDCLKRAFKIESDACNSCPYCRKEMNKSCL 741
L + C IC++ P+ C HTFC C++R + CP CR E +S L
Sbjct: 20 LYPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQP----KCPLCRAEDQESKL 75
Query: 742 ETHSNDALQSILSTLFPGYSSAR 764
SN + I+ + + R
Sbjct: 76 R--SNWLVSEIVE----SFKNLR 92
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 39.3 bits (92), Expect = 2e-04
Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 6/54 (11%)
Query: 687 EKFLCIICQELVYKPITLDCVHT-FCHDCLKRAFKIESDACNSCPYCRKEMNKS 739
E LC+IC E + L C H C +C KR CP CR+ +
Sbjct: 1 EDDLCVICLERPRNVVFLPCGHLCLCEECAKRLRS-----KKKCPICRQPIESV 49
>gnl|CDD|185411 PTZ00044, PTZ00044, ubiquitin; Provisional.
Length = 76
Score = 39.4 bits (92), Expect = 4e-04
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 1 MYVKIRSLDGSKNCVLVLSKRTLISDMKTQIENTLDVPVDKQRLFYKGKQLEDEYMLFDY 60
M + I++L G K T + +K ++ + V + RL Y GKQ+ D+ L DY
Sbjct: 1 MQILIKTLTGKKQSFNFEPDNT-VQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDY 59
Query: 61 NVNLNDVIQLMIK 73
V I ++++
Sbjct: 60 KVVPGSTIHMVLQ 72
>gnl|CDD|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger). The
C3HC4 type zinc-finger (RING finger) is a cysteine-rich
domain of 40 to 60 residues that coordinates two zinc
ions, and has the consensus sequence:
C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C
where X is any amino acid. Many proteins containing a
RING finger play a key role in the ubiquitination
pathway.
Length = 40
Score = 38.2 bits (89), Expect = 4e-04
Identities = 13/43 (30%), Positives = 17/43 (39%), Gaps = 4/43 (9%)
Query: 691 CIICQE-LVYKPITLDCVHTFCHDCLKRAFKIESDACNSCPYC 732
C IC E L C H FC C+ + + +CP C
Sbjct: 1 CPICLEEPKDPVTILPCGHLFCSKCILSWLESGN---VTCPLC 40
>gnl|CDD|192903 pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-like. The
small ubiquitin-related modifier SUMO-1 is a Ub/Ubl
family member, and although SUMO-1 shares structural
similarity to Ub, SUMO's cellular functions remain
distinct insomuch as SUMO modification alters protein
function through changes in activity, cellular
localisation, or by protecting substrates from
ubiquitination. Rad60 family members contain
functionally enigmatic, integral SUMO-like domains
(SLDs). Despite their divergence from SUMO, each Rad60
SLD interacts with a subset of SUMO pathway enzymes:
SLD2 specifically binds the SUMO E2 conjugating enzyme
(Ubc9)), whereas SLD1 binds the SUMO E1 (Fub2, also
called Uba2) activating and E3 (Pli1, also called Siz1
and Siz2) specificity enzymes. Structural analysis of
PDB:2uyz reveals a mechanistic basis for the
near-synonymous roles of Rad60 and SUMO in survival of
genotoxic stress and suggest unprecedented
DNA-damage-response functions for SLDs in regulating
SUMOylation. The Rad60 branch of this family is also
known as RENi (Rad60-Esc2-Nip45), and biologically it
should be two distinct families SUMO and RENi
(Rad60-Esc2-Nip45).
Length = 72
Score = 37.5 bits (88), Expect = 0.001
Identities = 16/73 (21%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 1 MYVKIRSLDGSKNCVLVLSKRTLISDMKTQIENTLDVPV-DKQRLFYKGKQLEDEYMLFD 59
+ +K++ DG + + V T +S + +P + RL + G++L+ + D
Sbjct: 1 IRIKLKGKDGKEVFIKV-KPTTTLSKLINAYRKKRGIPADQQVRLIFDGERLDPNDTVAD 59
Query: 60 YNVNLNDVIQLMI 72
Y++ D I ++I
Sbjct: 60 YDIEDGDTIDVVI 72
>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23. All proteins
in this family for which functions are known are
components of a multiprotein complex used for targeting
nucleotide excision repair to specific parts of the
genome. In humans, Rad23 complexes with the XPC protein.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 378
Score = 40.6 bits (95), Expect = 0.002
Identities = 22/119 (18%), Positives = 45/119 (37%), Gaps = 19/119 (15%)
Query: 1 MYVKIRSLDGSKNCVLVLSKRTLISDMKTQIE---NTLDVPVDKQRLFYKGKQLEDEYML 57
M + ++L K + + + ++K +IE PV +Q+L Y GK L D+ +
Sbjct: 1 MTLTFKTLQQQK-FKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTV 59
Query: 58 FDYNVNLNDVIQLMIKADIDKNYQSSESSSKENIQPNGPACKPNINTENASSSGNNTEP 116
+Y + D + +M+ S + + P P +A + +
Sbjct: 60 KEYKIKEKDFVVVMV---------SKPKTGTGKVAP------PAATPTSAPTPTPSPPA 103
>gnl|CDD|176397 cd01802, AN1_N, ubiquitin-like domain of AN1. AN1 (also known as
ANUBL1 and RSD-7) is ubiquitin-like protein with a
testis-specific expression in rats that has an
N-terminal ubiquitin-like domain and a C-terminal
zinc-binding domain. Unlike ubiquitin polyproteins and
most ubiquitin fusion proteins, the N-terminal
ubiquitin-like domain of An1 does not undergo
proteolytic processing. The function of AN1 is
unknown.
Length = 103
Score = 36.4 bits (84), Expect = 0.009
Identities = 23/62 (37%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 1 MYVKIRSLDGSKNCVLVLSKRTLISDMKTQIENTLDVPVDKQRLFYKGKQLEDEYMLFDY 60
M + I +L G+ + V T+IS +K +I+ +PV +Q L + +LEDEY L DY
Sbjct: 28 MELFIETLTGTCFELRVSPFETVIS-VKAKIQRLEGIPVAQQHLIWNNMELEDEYCLNDY 86
Query: 61 NV 62
N+
Sbjct: 87 NI 88
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal
transduction mechanisms].
Length = 391
Score = 38.9 bits (90), Expect = 0.009
Identities = 18/78 (23%), Positives = 26/78 (33%), Gaps = 3/78 (3%)
Query: 682 LEHIQEKFLCIICQELVYKPITLDCVHTFCHDCLKRAFKIESDACNSC--PYCRKEMNKS 739
L+ + C IC + P C HTFC C++R C C C + S
Sbjct: 19 LKGLDSMLRCRICDCRISIPCETTCGHTFCSLCIRRHLG-TQPFCPVCREDPCESRLRGS 77
Query: 740 CLETHSNDALQSILSTLF 757
N++ L
Sbjct: 78 SGSREINESHARNRDLLR 95
>gnl|CDD|222135 pfam13445, zf-RING_LisH, RING-type zinc-finger, LisH dimerisation
motif. This zinc-finger is the dimerisation motif for
LisH proteins, and is also a typical RING-type of plant
ubiquitin ligases.
Length = 55
Score = 33.5 bits (77), Expect = 0.024
Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 684 HIQEKFLCIICQELVY----KPITLDCVHTFCHDCLKR 717
H F+C I +E++ P+ L C H + L++
Sbjct: 6 HFHSIFVCPISKEVMTDEENPPVMLPCGHVYSRKALEK 43
>gnl|CDD|225973 COG3440, COG3440, Predicted restriction endonuclease [Defense
mechanisms].
Length = 301
Score = 36.3 bits (84), Expect = 0.049
Identities = 12/52 (23%), Positives = 21/52 (40%)
Query: 438 SEAGVHRPHVSGIHGREDVGAFSLVLSGGYEDDVDDGDSFLYTGSGGRDLSG 489
EA H+P + GR+ F G YE ++ + L++ G +
Sbjct: 25 REAAPHKPILLLDVGRKISTFFITENQGIYETELIEPFIQLWSFFGPKLQKY 76
>gnl|CDD|188119 TIGR01206, lysW, lysine biosynthesis protein LysW. This very
small, poorly characterized protein has been shown
essential in Thermus thermophilus for an unusual pathway
of Lys biosynthesis from aspartate by way of
alpha-aminoadipate (AAA) rather than diaminopimelate. It
is found also in Deinococcus radiodurans and Pyrococcus
horikoshii, which appear to share the AAA pathway [Amino
acid biosynthesis, Aspartate family].
Length = 54
Score = 32.2 bits (73), Expect = 0.084
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 314 CKDCGCSICAGKTSPDKLIVCEECQHYYHIWCLKPP-LESVPEDDE 358
C DCG I +L++C+EC + L P LE PE+ E
Sbjct: 5 CPDCGAEIELENPELGELVICDECGAELEVVSLDPLRLEQAPEEAE 50
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 34.9 bits (80), Expect = 0.11
Identities = 17/56 (30%), Positives = 22/56 (39%), Gaps = 3/56 (5%)
Query: 679 KEVLEHIQEK-FLCIICQELVYKPITLDCVHTFCHDCLKRAFKIESDACNSCPYCR 733
K L I + C +C E P C H FC CL ++ + CP CR
Sbjct: 205 KNGLPFIPLADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKK--YEFCPLCR 258
>gnl|CDD|227481 COG5152, COG5152, Uncharacterized conserved protein, contains RING
and CCCH-type Zn-fingers [General function prediction
only].
Length = 259
Score = 34.7 bits (79), Expect = 0.16
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 689 FLCIICQELVYKPITLDCVHTFCHDCLKRAFKIESDACNSC 729
FLC IC++ P+ +C H+FC C R ++ + D C C
Sbjct: 197 FLCGICKKDYESPVVTECGHSFCSLCAIRKYQ-KGDECGVC 236
>gnl|CDD|240257 PTZ00073, PTZ00073, 60S ribosomal protein L37; Provisional.
Length = 91
Score = 32.4 bits (74), Expect = 0.16
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 708 HTFCHDCLKRAFKIESDACNSCPYCRKEM 736
HT C C KR+F ++ C SC Y +M
Sbjct: 16 HTLCRRCGKRSFHVQKKRCASCGYPSAKM 44
>gnl|CDD|176389 cd01794, DC_UbP_C, dendritic cell derived ubiquitin-like protein.
DC_UbP (dendritic cell derived ubiquitin-like protein)
is a ubiquitin-like protein from human dendritic cells
that is expressed in the mitochondrion. The
ubiquitin-like domain of this protein is found at the
C-terminus and lacks the canonical gly-gly motif of
ubiquitin required for ubiquitinization. DC_UbP is
expressed in tumor cells but not in normal human adult
tissue suggesting a role for DC_UbP in tumorogenesis.
Length = 70
Score = 31.0 bits (70), Expect = 0.32
Identities = 17/69 (24%), Positives = 33/69 (47%)
Query: 4 KIRSLDGSKNCVLVLSKRTLISDMKTQIENTLDVPVDKQRLFYKGKQLEDEYMLFDYNVN 63
L K+ L +S + + +K Q++ V QR F+ GK L D+ L + +
Sbjct: 1 LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFSGKLLTDKTRLQETKIQ 60
Query: 64 LNDVIQLMI 72
+ V+Q+++
Sbjct: 61 KDYVVQVIV 69
>gnl|CDD|204746 pfam11793, FANCL_C, FANCL C-terminal domain. This domain is found
at the C-terminus of the Fancl protein in humans which
is the putative E3 ubiquitin ligase subunit of the FA
complex (Fanconi anaemia). Eight subunits of the Fanconi
anaemia gene products form a multisubunit nuclear
complex which is required for mono-ubiquitination of a
downstream FA protein, FANCD2.
Length = 70
Score = 30.5 bits (69), Expect = 0.41
Identities = 18/64 (28%), Positives = 24/64 (37%), Gaps = 10/64 (15%)
Query: 310 ETKHCKDCGCSICAGKTSPDKLIVCEE--CQHYYHIWCLKPPLESVPEDDEWF------C 361
C C G PD I C+ C +HI CL L ++ + + F C
Sbjct: 1 FEIECGICYAYRLDGGEIPD--ISCDNPKCGLPFHIACLYEWLRTLRDSRQSFNVSFGTC 58
Query: 362 PSCK 365
P CK
Sbjct: 59 PYCK 62
>gnl|CDD|176388 cd01793, Fubi, Fubi ubiquitin-like protein. Fubi is a
ubiquitin-like protein encoded by the fau gene which
has an N-terminal ubiquitin-like domain (also referred
to as FUBI) fused to the ribosomal protein S30. Fubi
is thought to be a tumor suppressor protein and the
FUBI domain may act as a substitute or an inhibitor of
ubiquitin or one of ubiquitin's close relatives UCRP,
FAT10, and Nedd8.
Length = 74
Score = 30.1 bits (68), Expect = 0.65
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 24 ISDMKTQIENTLDVPVDKQRLFYKGKQLEDEYML 57
+SD+K + + V+ Q L G LED+ L
Sbjct: 21 VSDIKAHVAGLEGIDVEDQVLLLAGVPLEDDATL 54
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 32.4 bits (74), Expect = 0.65
Identities = 19/53 (35%), Positives = 24/53 (45%), Gaps = 12/53 (22%)
Query: 691 CIICQELVY-KP-------ITLDCVHTFCHDCLKRAFKIESDACNSCPYCRKE 735
C IC E VY K I +C H FC +C+ K + N+CP CR
Sbjct: 177 CAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEK----NTCPVCRTP 225
>gnl|CDD|152056 pfam11620, GABP-alpha, GA-binding protein alpha chain. This
family of proteins represents the transcription factor
GABP alpha. This alpha domain is a five-stranded
beta-sheet crossed by a distorted helix termed an OST
domain. The surface of the GABP alpha OST domain
contains two clusters of negatively-charged residues
suggesting there are positively-charged partner
proteins. The OST domain binds to the CH1 and CH3
domains of the co-activator histone acetyltransferase
CBP/p300, a direct link between GABP and
transcriptional machinery has been made.
Length = 86
Score = 30.1 bits (68), Expect = 0.96
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 21 RTLISDMKTQIENTLDVPVDKQRLFYKGKQLEDEYMLFDYNVNLNDVIQLMIKADIDKNY 80
R I ++K +E L V +DK ++ + QLE + LFD V ++QL ++
Sbjct: 11 REPIGNLKKLLEPRLQVSLDKYDIWLQDIQLEPDKSLFDQGVKGEGLVQLSVQV------ 64
Query: 81 QSSESSSKENI 91
Q+S K NI
Sbjct: 65 QTSSGEPKLNI 75
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 31.9 bits (72), Expect = 1.4
Identities = 18/63 (28%), Positives = 24/63 (38%), Gaps = 3/63 (4%)
Query: 686 QEKFLCIICQELVYKPITLDCVHTFCHDCLKRAFKIESDACNSCPYCRKEMNKSCLETHS 745
+E C IC C H CH C R + CP CR E ++ + T S
Sbjct: 59 EENMNCQICAGSTTYSARYPCGHQICHACAVRLRALYMQ--KGCPLCRTE-TEAVVFTAS 115
Query: 746 NDA 748
+ A
Sbjct: 116 SPA 118
>gnl|CDD|202539 pfam03107, C1_2, C1 domain. This short domain is rich in cysteines
and histidines. The pattern of conservation is similar
to that found in pfam00130, therefore we have termed
this domain DC1 for divergent C1 domain. This domain
probably also binds to two zinc ions. The function of
proteins with this domain is uncertain, however this
domain may bind to molecules such as diacylglycerol (A
Bateman pers. obs.). This family are found in plant
proteins.
Length = 30
Score = 27.6 bits (62), Expect = 1.6
Identities = 8/27 (29%), Positives = 12/27 (44%)
Query: 319 CSICAGKTSPDKLIVCEECQHYYHIWC 345
CS+C K C++C H+ C
Sbjct: 3 CSVCRRKIDGFYFYTCKKCCFTLHVRC 29
>gnl|CDD|145613 pfam02568, ThiI, Thiamine biosynthesis protein (ThiI). ThiI is
required for thiazole synthesis, required for thiamine
biosynthesis.
Length = 197
Score = 30.8 bits (70), Expect = 1.6
Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 9/45 (20%)
Query: 665 NVWDEIKALC---------KEGQKEVLEHIQEKFLCIICQELVYK 700
+ E C + QKE++E EK+ C++C+ +Y+
Sbjct: 54 ELLAEYGTSCEGKLVVVDFTKVQKEIIEKAPEKYRCVLCKRCMYR 98
>gnl|CDD|238210 cd00350, rubredoxin_like, Rubredoxin_like; nonheme iron binding
domain containing a [Fe(SCys)4] center. The family
includes rubredoxins, a small electron transfer protein,
and a slightly smaller modular rubredoxin domain present
in rubrerythrin and nigerythrin and detected either N-
or C-terminal to such proteins as flavin reductase,
NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin
reductase. In rubredoxin, the iron atom is coordinated
by four cysteine residues (Fe(S-Cys)4), but iron can
also be replaced by cobalt, nickel or zinc and believed
to be involved in electron transfer. Rubrerythrins and
nigerythrins are small homodimeric proteins, generally
consisting of 2 domains: a rubredoxin domain C-terminal
to a non-sulfur, oxo-bridged diiron site in the
N-terminal rubrerythrin domain. Rubrerythrins and
nigerythrins have putative peroxide activity.
Length = 33
Score = 27.5 bits (62), Expect = 1.8
Identities = 9/38 (23%), Positives = 12/38 (31%), Gaps = 11/38 (28%)
Query: 333 VCEECQHYYHIWCLKPPLESVPEDDEWFCPSCKRDTSE 370
VC C + Y E+ W CP C +
Sbjct: 3 VCPVCGYIYD-----------GEEAPWVCPVCGAPKDK 29
>gnl|CDD|176407 cd01812, BAG1_N, Ubiquitin-like domain of BAG1. BAG1_N
N-terminal ubiquitin-like (Ubl) domain of the BAG1
protein. This domain occurs together with the BAG
domain and is closely related to the Ubl domain of a
family of deubiquitinases that includes Rpn11, UBP6
(USP14), USP7 (HAUSP).
Length = 71
Score = 28.4 bits (64), Expect = 2.2
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 26 DMKTQIENTLDVPVDKQRLFYKGKQLED 53
D+K + V Q+L +KGK+ +D
Sbjct: 24 DLKKMLAPVTGVEPRDQKLIFKGKERDD 51
>gnl|CDD|165237 PHA02926, PHA02926, zinc finger-like protein; Provisional.
Length = 242
Score = 30.8 bits (69), Expect = 2.2
Identities = 29/87 (33%), Positives = 40/87 (45%), Gaps = 15/87 (17%)
Query: 658 NNDTVHSNVWDEIKALCKEGQKEVLEHIQEKFLCIICQELVYKP---------ITLDCVH 708
NN T S + D IK L K ++V +EK C IC E+VY + C H
Sbjct: 144 NNTTTISEL-DIIKILDK--YEDVYRVSKEK-ECGICYEVVYSKRLENDRYFGLLDSCNH 199
Query: 709 TFCHDCLK--RAFKIESDACNSCPYCR 733
FC C+ + E+ A ++CP CR
Sbjct: 200 IFCITCINIWHRTRRETGASDNCPICR 226
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 30.9 bits (70), Expect = 2.7
Identities = 30/123 (24%), Positives = 51/123 (41%), Gaps = 11/123 (8%)
Query: 568 VKGSSDFIVWRFHL----QRDDEAPAPWTEEGKKRIKDLGLQMIYPEGYEEAQAAKEASK 623
VK S+FI + +L + + E P EE K+ K+ + + E + ++ K
Sbjct: 12 VKKHSEFINYPIYLWVEKEVEKEVPDEEEEEEKEEKKEEE-EKTTDKEEEVDEEEEKEEK 70
Query: 624 ANLKRKVSSETLGESKVKKSKQVYT-LPSSVLEHINNDTVHS--NVWDE---IKALCKEG 677
+KV T + K+K ++T P V + S N W++ +K EG
Sbjct: 71 KKKTKKVKETTTEWELLNKTKPIWTRNPKDVTKEEYAAFYKSLTNDWEDPLAVKHFSVEG 130
Query: 678 QKE 680
Q E
Sbjct: 131 QLE 133
>gnl|CDD|238022 cd00065, FYVE, FYVE domain; Zinc-binding domain; targets proteins
to membrane lipids via interaction with
phosphatidylinositol-3-phosphate, PI3P; present in Fab1,
YOTB, Vac1, and EEA1;.
Length = 57
Score = 27.8 bits (62), Expect = 2.9
Identities = 13/53 (24%), Positives = 19/53 (35%), Gaps = 15/53 (28%)
Query: 300 VPECTTC----NDVETK-HCKDCG---CSICAGKTSP-------DKLIVCEEC 337
C C + HC++CG CS C+ P + VC+ C
Sbjct: 2 ASSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPLPSMGGGKPVRVCDSC 54
>gnl|CDD|131283 TIGR02228, sigpep_I_arch, signal peptidase I, archaeal type. This
model represents signal peptidase I from most archaea, a
subunit of the eukaryotic endoplasmic reticulum signal
peptidase I complex, and an apparent signal peptidase I
from a small number of bacteria. It is related to but
does not overlap in hits with TIGR02227, the bacterial
and mitochondrial signal peptidase I.
Length = 158
Score = 29.7 bits (67), Expect = 2.9
Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 8/52 (15%)
Query: 115 EPE----DFVDLKPADSQYYKVGDYVDAILETEGAWFESQITHILVDINKEK 162
EP D + + AD +VGD + +TH +++IN
Sbjct: 42 EPTFNTGDLILVTGADPNDIQVGDVITYKSPGFNTP----VTHRVIEINNSG 89
>gnl|CDD|221705 pfam12678, zf-rbx1, RING-H2 zinc finger. There are 8 cysteine/
histidine residues which are proposed to be the
conserved residues involved in zinc binding. The
protein, of which this domain is the conserved region,
participates in diverse functions relevant to chromosome
metabolism and cell cycle control.
Length = 73
Score = 28.2 bits (63), Expect = 3.0
Identities = 14/56 (25%), Positives = 19/56 (33%), Gaps = 17/56 (30%)
Query: 691 CIICQELVYKP-------------ITLDCVHTFCHDCLKRAFKIESDACNSCPYCR 733
C IC+ + +C H F C+ R K N+CP CR
Sbjct: 22 CAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTR----NTCPLCR 73
>gnl|CDD|224236 COG1317, FliH, Flagellar biosynthesis/type III secretory pathway
protein [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 234
Score = 30.1 bits (68), Expect = 3.5
Identities = 14/63 (22%), Positives = 21/63 (33%), Gaps = 9/63 (14%)
Query: 580 HLQRDDEAPAPWTEEGKKRIKDLGLQMIYPEGYEEAQAAKEASK---------ANLKRKV 630
Q E EG + LG + + EG EE + + +K LK V
Sbjct: 56 AAQELQEGIEEGAREGYEEGFQLGYEEGFEEGQEEGRVLERLAKLIAEFQAELEALKEVV 115
Query: 631 SSE 633
+
Sbjct: 116 EKQ 118
>gnl|CDD|238372 cd00730, rubredoxin, Rubredoxin; nonheme iron binding domains
containing a [Fe(SCys)4] center. Rubredoxins are small
nonheme iron proteins. The iron atom is coordinated by
four cysteine residues (Fe(S-Cys)4), but iron can also
be replaced by cobalt, nickel or zinc. They are believed
to be involved in electron transfer.
Length = 50
Score = 27.3 bits (61), Expect = 3.8
Identities = 12/46 (26%), Positives = 17/46 (36%), Gaps = 10/46 (21%)
Query: 333 VCEECQHYYH------IWCLKP--PLESVPEDDEWFCPSCKRDTSE 370
C C + Y + P P E +P+D W CP C +
Sbjct: 3 ECRICGYIYDPAEGDPDEGIPPGTPFEDLPDD--WVCPVCGAGKDD 46
>gnl|CDD|215998 pfam00567, TUDOR, Tudor domain.
Length = 118
Score = 28.9 bits (65), Expect = 3.8
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 15/78 (19%)
Query: 122 LKPADSQYYKVGDYVDAILETEGAWFESQITHILVDINKEKPYDEDDLIFKVVHLKYKDD 181
KP +S KVGD A +G W+ ++I LV ++ V + + D
Sbjct: 41 SKPPESLPPKVGDGCVAAFSEDGKWYRAKI---LVSLDDGL-----------VEVFFIDY 86
Query: 182 GSS-TMKFDDIRPLPKHL 198
G++ T+ D+RPLP
Sbjct: 87 GNTETVPLSDLRPLPSEF 104
>gnl|CDD|129553 TIGR00461, gcvP, glycine dehydrogenase (decarboxylating). This
apparently ubiquitous enzyme is found in bacterial,
mammalian and plant sources. The enzyme catalyzes the
reaction: GLYCINE + LIPOYLPROTEIN =
S-AMINOMETHYL-DIHYDROLIPOYLPROTEIN + CO2. It is part of
the glycine decarboxylase multienzyme complex (GDC)
consisting of four proteins P, H, L and T. Active site
in E.coli is located as the (K) residues at position 713
of the SEED alignment [Energy metabolism, Amino acids
and amines].
Length = 939
Score = 30.7 bits (69), Expect = 3.8
Identities = 19/59 (32%), Positives = 22/59 (37%), Gaps = 1/59 (1%)
Query: 609 PEGYEEAQAAKEASKANLKRKVSSETLGESKVKKSKQVYTLPSSVLE-HINNDTVHSNV 666
P GY AA A K RK+ +G SK L E HI D SN+
Sbjct: 259 PMGYGGPHAAFFAVKDEYNRKMPGRIVGVSKDALGNTALRLALQTREQHIRRDKATSNI 317
>gnl|CDD|237280 PRK13034, PRK13034, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 29.9 bits (68), Expect = 5.4
Identities = 9/37 (24%), Positives = 17/37 (45%)
Query: 639 KVKKSKQVYTLPSSVLEHINNDTVHSNVWDEIKALCK 675
+ +++ VL+ + N + V E+KALC
Sbjct: 375 GEAEFREIANWILDVLDDLGNAALEQRVRKEVKALCS 411
>gnl|CDD|184477 PRK14052, PRK14052, effector protein; Provisional.
Length = 387
Score = 29.9 bits (67), Expect = 6.0
Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 1/63 (1%)
Query: 615 AQAAKEA-SKANLKRKVSSETLGESKVKKSKQVYTLPSSVLEHINNDTVHSNVWDEIKAL 673
AQ E + +L + V +E L E K+ + + IN T N + I AL
Sbjct: 207 AQRHIEGLASTDLSQGVYAEGLAEDAFNKNGVTDNVERAAAWIINASTSKGNDAENITAL 266
Query: 674 CKE 676
KE
Sbjct: 267 LKE 269
>gnl|CDD|220784 pfam10497, zf-4CXXC_R1, Zinc-finger domain of monoamine-oxidase A
repressor R1. R1 is a transcription factor repressor
that inhibits monoamine oxidase A gene expression. This
domain is a four-CXXC zinc finger putative DNA-binding
domain found at the C-terminal end of R1. The domain
carries 12 cysteines of which four pairs are of the CXXC
type.
Length = 105
Score = 28.2 bits (63), Expect = 6.2
Identities = 12/48 (25%), Positives = 18/48 (37%), Gaps = 7/48 (14%)
Query: 325 KTSPDKLIVCEECQHYYHIWCLK-------PPLESVPEDDEWFCPSCK 365
KTS +EC +C K + +D +W CP C+
Sbjct: 21 KTSCKDKKKGKECHGVRGQFCGKCLRNRYGENADEAAKDPDWICPPCR 68
>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 427
Score = 29.7 bits (66), Expect = 7.0
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 691 CIICQELVYKPI-TLDCVHTFCHDCLKRAFKIESDACNSCPYCRKE 735
C +C L+ P+ T C HTFC +C+ A ++SD CP C ++
Sbjct: 277 CPLCHCLLRNPMKTPCCGHTFCDECIGTAL-LDSDF--KCPNCSRK 319
>gnl|CDD|178747 PLN03208, PLN03208, E3 ubiquitin-protein ligase RMA2; Provisional.
Length = 193
Score = 28.9 bits (64), Expect = 7.5
Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 12/65 (18%)
Query: 689 FLCIICQELVYKPITLDCVHTFCHDCLKRAFKIESDACN------------SCPYCRKEM 736
F C IC + V P+ C H FC C+ + +++ CP C+ ++
Sbjct: 19 FDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDV 78
Query: 737 NKSCL 741
+++ L
Sbjct: 79 SEATL 83
>gnl|CDD|200474 cd11335, AmyAc_MTase_N, Alpha amylase catalytic domain found in
maltosyltransferase. Maltosyltransferase (MTase), a
maltodextrin glycosyltransferase, acts on starch and
maltooligosaccharides. It catalyzes the transfer of
maltosyl units from alpha-1,4-linked glucans or
maltooligosaccharides to other alpha-1,4-linked glucans,
maltooligosaccharides or glucose. MTase is a homodimer.
The catalytic core domain has the (beta/alpha) 8 barrel
fold with the active-site cleft formed at the C-terminal
end of the barrel. Substrate binding experiments have
led to the location of two distinct maltose-binding
sites: one lies in the active-site cleft and the other
is located in a pocket adjacent to the active-site
cleft. It is a member of the alpha-amylase family, but
unlike typical alpha-amylases, MTase does not require
calcium for activity and lacks two histidine residues
which are predicted to be critical for binding the
glucose residue adjacent to the scissile bond in the
substrates. The common reaction chemistry of the
alpha-amylase family of enzymes is based on a two-step
acid catalytic mechanism that requires two critical
carboxylates: one acting as a general acid/base (Glu)
and the other as a nucleophile (Asp). Both hydrolysis
and transglycosylation proceed via the nucleophilic
substitution reaction between the anomeric carbon, C1
and a nucleophile. The Alpha-amylase family comprises
the largest family of glycoside hydrolases (GH), with
the majority of enzymes acting on starch, glycogen, and
related oligo- and polysaccharides. These proteins
catalyze the transformation of alpha-1,4 and alpha-1,6
glucosidic linkages with retention of the anomeric
center. The protein is described as having 3 domains: A,
B, C. A is a (beta/alpha) 8-barrel; B is a loop between
the beta 3 strand and alpha 3 helix of A; C is the
C-terminal extension characterized by a Greek key. The
majority of the enzymes have an active site cleft found
between domains A and B where a triad of catalytic
residues (Asp, Glu and Asp) performs catalysis. Other
members of this family have lost the catalytic activity
as in the case of the human 4F2hc, or only have 2
residues that serve as the catalytic nucleophile and the
acid/base, such as Thermus A4 beta-galactosidase with 2
Glu residues (GH42) and human alpha-galactosidase with 2
Asp residues (GH31). The family members are quite
extensive and include: alpha amylase,
maltosyltransferase, cyclodextrin glycotransferase,
maltogenic amylase, neopullulanase, isoamylase,
1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 538
Score = 29.6 bits (67), Expect = 7.7
Identities = 8/46 (17%), Positives = 18/46 (39%), Gaps = 5/46 (10%)
Query: 653 VLEHI-----NNDTVHSNVWDEIKALCKEGQKEVLEHIQEKFLCII 693
V EH+ + + + W + + + L I+++F C
Sbjct: 221 VKEHLKLFRWSPNKIDPEKWRNFFKENPKPEGDFLGEIEKEFGCTT 266
>gnl|CDD|226801 COG4357, COG4357, Zinc finger domain containing protein (CHY type)
[Function unknown].
Length = 105
Score = 27.9 bits (62), Expect = 8.4
Identities = 12/30 (40%), Positives = 14/30 (46%)
Query: 711 CHDCLKRAFKIESDACNSCPYCRKEMNKSC 740
C C K + E C SCPYC+ N C
Sbjct: 65 CGVCRKLLTRAEYGMCGSCPYCQSPFNPGC 94
>gnl|CDD|225787 COG3248, Tsx, Nucleoside-binding outer membrane protein [Cell
envelope biogenesis, outer membrane].
Length = 284
Score = 29.1 bits (65), Expect = 8.8
Identities = 18/54 (33%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 433 YRFQASEAGVHRPHVSGIHGREDVGAFSLVLSGGYEDD--VDDGDSFLYTGSGG 484
R S A H ++ H V A G + DD + DGD F TG GG
Sbjct: 223 TRTNNSIASSHILALNYDHWHYSVVARYWHDGGQWNDDYGLKDGDGFKSTGWGG 276
>gnl|CDD|222758 pfam14446, Prok-RING_1, Prokaryotic RING finger family 1. RING
finger family found sporadically in bacteria and
archaea, and associated in gene neighborhoods with other
components of the ubiquitin-based signaling and
degradation system, including ubiquitin, the E1 and E2
proteins and the JAB-like metallopeptidase. The
bacterial versions contain transmembrane helices.
Length = 55
Score = 26.3 bits (58), Expect = 9.3
Identities = 12/28 (42%), Positives = 13/28 (46%), Gaps = 1/28 (3%)
Query: 319 CSICAGKTSPDKLIV-CEECQHYYHIWC 345
C +C K P IV C EC YH C
Sbjct: 8 CPVCGKKFKPGDDIVVCPECGAPYHREC 35
>gnl|CDD|239449 cd03333, chaperonin_like, chaperonin_like superfamily. Chaperonins
are involved in productive folding of proteins. They
share a common general morphology, a double toroid of 2
stacked rings, each composed of 7-9 subunits. There are
2 main chaperonin groups. The symmetry of type I is
seven-fold and they are found in eubacteria (GroEL) and
in organelles of eubacterial descent (hsp60 and RBP).
The symmetry of type II is eight- or nine-fold and they
are found in archea (thermosome), thermophilic bacteria
(TF55) and in the eukaryotic cytosol (CTT). Their
common function is to sequester nonnative proteins
inside their central cavity and promote folding by using
energy derived from ATP hydrolysis. This superfamily
also contains related domains from Fab1-like
phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases
that only contain the intermediate and apical domains.
Length = 209
Score = 28.6 bits (65), Expect = 9.9
Identities = 17/50 (34%), Positives = 22/50 (44%), Gaps = 6/50 (12%)
Query: 220 PRERGYWHDMI-IEKKQGKRLT-TELIATVFIGK----KGLETRLENCKI 263
P R +I +EK G L +EL+ V K + RLEN KI
Sbjct: 36 PDNRMDDLGVIKVEKIPGGSLEDSELVVGVVFDKGYASPYMPKRLENAKI 85
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.134 0.403
Gapped
Lambda K H
0.267 0.0701 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 37,688,476
Number of extensions: 3657605
Number of successful extensions: 3433
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3409
Number of HSP's successfully gapped: 85
Length of query: 764
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 660
Effective length of database: 6,324,786
Effective search space: 4174358760
Effective search space used: 4174358760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 63 (28.1 bits)